Bioconductor Changelog

flowViz

lpolygon methods now return the gate outlines and the contour function is fixed

flowCore

added parameters method for filterResults
Changed the introduction a little and added a few sentences about plateCore.

Biostrings

Added the read.rmMask() and read.trfMask() functions for reading a mask from a RepeatMasker .out file or from a Tandem Repeats Finder .bed file. No version bump yet.
Added score profiles to pairwiseAligment results to allow users to see how well strings align at different points.

Rintact

i have added the man page
i have added a new method to the package

annotate

Changed useHomology vignette so it won't interfere with build. Will replace with a new version soon.

Biostrings

Added the maskMotif() generic function for masking a sequence by content.
As a consequence, previous 'masks(x) <- "motif"' syntax must be replaced by
new 'x <- maskMotif(x, "motif")' syntax.
Bumped version to 2.9.3

vsn

I added a section to the vignette about the relationship between vsn
parameters and the additive-multiplicative error model.

ontoTools

xcmsGUI

This just creates an empty project for xcmsGUI

arrayQualityMetrics

Correcting the legend when using grouprep =TRUE

oligoClasses

Bug fix: initialize for SnpCopyNumberSet

flowCore

small work on the text and add references

Biostrings

Added the coverage() generic function with methods for IRanges, MaskCollection, XStringViews, MaskedXString and MIndex objects. Version bumped to 2.9.2
Changed the algorithm in pairwiseAlignment to start at the end of the strings rather than the beginning to make it easier to get the scores based on alignment starts.
First pass as reworking the pairwiseAlignment infrastructure to use less memory. It is also marginally faster as well.

BiocCaseStudies

cleaned up Description

GGtools

supp2SQLite

EBImage

New EBImage.dll compiled with R2.7.0, GTK 2.12.9 and ImageMagick 6.4.1

Biostrings

First pass as reworking the pairwiseAlignment infrastructure to use less memory. It is also marginally faster as well.

spkTools

Adding vignette

GGtools

new support function
improved supp2SQLite
make sure it orders chromsomes suitably

EBImage

New EBImage.dll compiled with R2.7.0, GTK 2.12.9 and ImageMagick 6.4.1

ShortRead

Revised sample data
Revised sample data
AlignedRead class
- class definition
- AlignedDataFrame, extending AnnotatedDataFrame, for additional
alignment information
files) into XStringSet objects
clean generic to trim non-nucleotide sequences

CMA

Adds CMA to the 2.3 bioconductor repository.

GGtools

minor changes to getAlleles for robustness
tweak plot_EvG which can generate a dataframe in an inopportune point

ShortRead

'scripts' directory

CMA

Adds CMA to the 2.3 bioconductor repository.

affxparser

moved the updates from release to devel

LPEadj

changed version to 1.0.0

xcms

Migrate to ncdf for xcmsRaw.write()
changed part about xcmsRaw return value. via Colin

arrayQualityMetrics

- add argument grouprep for group representation. It allows to show the
boxplots and densityplots with colours according to their biological
group defined in intgroup.

GGtools

tweak plot_EvG which can generate a dataframe in an inopportune point

flowClust

update README instructions for Windows users; move README to inst directory

limma

Reversing changes committed in error to plots-ms.R on 9 March 2008.

Biobase

AnnotatedDataFrame made more friendly to subclassing
- previously, a subclass would often be coerced to AnnotatedDataFrame
during, e.g., subsetting
combine,matrix,matrix-method bug fix
- non-overlapping rows and columns in the second matrix were NA,
rather than the value in the second matrix
- typo in vignett

flowClust

update README instructions for Windows users
minor change to Makevars.win

limma

Reversing changes committed in error to plots-ms.R on 9 March 2008.

flowCore

fixed some typos
more specific about sotware imports now
manuscript.tex now holds the actual paper
illustration and citation

Biostrings

Better fix for adjacentViews.
Fixed a bug in adjacentViews to allow the handling of character vectors.

CGHregions

Adds CGHbase and CGHregions to Bioc 2.3 repository.

LPEadj

Added LPEadj to Bioc 2.3 Repository.

plateCore

Working on making a density plot for flowPlates.